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Crystal structure of zebrafish prostacyclin synthase (cytochrome P450 8A1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IAG PDB ENTRY 2IAG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 1 microliter of concentrated protein solution (20mg/ml) in gel filtration buffer (20mM Tris-HCl pH 8.0, 150mM NaCl and 5mM beta-mercaptoethanol) was mixed with equal amount of reservoir solution (20% PEG 3350 plus either 50mM Tris-HCl (pH 8.0) or 50mM HEPES (Na-salt; pH 7.5)) and equilibrated against 450 microliter of reservoir solution at 277 K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.24 45.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.667 α = 90 b = 87.896 β = 90 c = 190.854 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 Toroidal FM 2006-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.08 30 99.9 0.046 18 5.4 60147 60087 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.08 2.15 99.8 0.21 4.3 5.4 5912
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2IAG 2.08 30 1 1 60147 56980 3031 99.81 0.22921 0.229 0.22735 0.26414 0.2619 RANDOM 28.442
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.5 -0.06 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.333 r_dihedral_angle_4_deg 18.495 r_dihedral_angle_3_deg 15.895 r_dihedral_angle_1_deg 5.289 r_scangle_it 2.48 r_mcangle_it 2.375 r_scbond_it 1.69 r_mcbond_it 1.533 r_angle_refined_deg 1.09 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.333 r_dihedral_angle_4_deg 18.495 r_dihedral_angle_3_deg 15.895 r_dihedral_angle_1_deg 5.289 r_scangle_it 2.48 r_mcangle_it 2.375 r_scbond_it 1.69 r_mcbond_it 1.533 r_angle_refined_deg 1.09 r_nbtor_refined 0.297 r_nbd_refined 0.186 r_symmetry_vdw_refined 0.183 r_symmetry_hbond_refined 0.123 r_xyhbond_nbd_refined 0.116 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7075 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing